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Re: [h5md-user] Periodic and non-periodic boundary conditions

From: Peter Colberg
Subject: Re: [h5md-user] Periodic and non-periodic boundary conditions
Date: Thu, 30 May 2013 22:19:06 -0400
User-agent: Mutt/1.5.21 (2010-09-15)

Hi Pierre,

On Wed, May 29, 2013 at 10:17:04AM +0200, Pierre de Buyl wrote:
> On Mon, May 06, 2013 at 11:18:15AM -0400, Peter Colberg wrote:
> > Let's start with an initial choice of "nonperiodic" and "periodic".
> > 
> > (See variable-length string array attribute [1] for implementation hint.)
> > 
> > LAMMPS has a non-periodic “shrink-wrapped” boundary condition [2],
> > where the walls follow the extent of all particles. These boundaries
> > are not "fixed", but still "nonperiodic".
> > 
> > [1] http://www.hdfgroup.org/ftp/HDF5/examples/misc-examples/attrvstr.c
> > [2] http://lammps.sandia.gov/doc/boundary.html
> For now, we should not take into account all kind of boundary conditions. The
> purpose, for now, is to identify correctly the geometry.
> Merging this issue with the box image vectors, what could be done is the
> following:
>   - Have "image" as an optional dataset in a trajectory.
>   - The presence of image implies periodicity.
>   - Partial periodicity is handled by having the image vectors equal 0 in the
>     corresponding dimension.
> This is simple and does not encumber the specification too much.

See the discussion of the “box/type” attribute, and a post by Konrad:


The same reasoning applies here: It is not sufficient to check whether
the image coordinate is zero or non-zero, since it may happen to be
zero at some times, despite a periodic dimension.

The information about periodicity is necessary for calculating the
distance between particles, e.g., to display a cluster of particles
relative to a common center of mass point.


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